The northeastern Adriatic is a shallow (depth up to 40 m), northernmost coastal area of the Mediterranean. The region is significantly influenced by riverine freshwater inputs and the established circulation patterns of the Adriatic Sea, characterised primarily by inflows of high-salinity water from the south, transported by the Eastern Adriatic Current (EAC). As a result, steep ecological gradients, driven mainly by rapid, pronounced spatial and temporal variations in environmental parameters, are present in the northeastern Adriatic. Therefore, complex monitoring approaches and advanced data acquisition are necessary for reliable assessments of this dynamic marine ecosystem. During a perennial (5-year) case study, designed to test and improve the existing monitoring approach for the area, the detailed dataset obtained for salinity, temperature, and oxygen concentration enabled the characterisation of measurement trends and the detection of environmental changes in the region. The expansion of the monitoring area, the increase in measurement frequency, and the implementation of new, modern measuring techniques and instruments (oceanographic buoy) have contributed to creating a robust, reliable dataset for present state analyses and future environmental predictions in the northeastern Adriatic.

The northern Adriatic is a highly dynamic marine ecosystem where multiple environmental stressors, particularly phosphorus limitation, shape phytoplankton communities. Previous studies have established annual phytoplankton succession patterns primarily using light microscopy, while metatranscriptomic analyses have been lacking. This study used a metatranscriptomic approach to investigate the taxonomic and functional dynamics of the northern Adriatic phytoplankton community, focusing on the predominant group of dinoflagellates. Monthly sampling from April 2021 to March 2022 at two coastal stations revealed dinoflagellates as the most metabolically active phylum throughout the year in the size fraction > 50 μm. Peaks in metabolic activity of other studied phyla aligned with the characteristic seasonal species succession observed in previous studies. Community ordination indicated distinct seasonal shifts driven by environmental factors, notably phosphorus and silicon availability, as well as species interactions. Both photosynthesis and phagotrophy emerged as important trophic strategies for dinoflagellates. Nitrogen and phosphorus metabolism showed clear seasonal trends, with dinoflagellates employing various strategies for nutrient acquisition and recycling depending on resource availability. Changes in the activation of different cellular processes highlighted a seasonal shift in metabolic investment, with spring favouring rapid population expansion, while the rest of the year was characterised by prevalent transcription of genes indicative of cellular maintenance and adaptation. This study provides critical new insights into dinoflagellate phytoplankton ecology and emphasises the need for further multi-method research to fully understand their role in the northern Adriatic ecosystem.

Over the past two decades, omics approaches have been widely applied to investigate the molecular diversity and physiological responses of marine eukaryotic phytoplankton to changing environmental conditions. The northern Adriatic stands as a highly dynamic marine ecosystem in which multiple environmental stressors and steep ecological gradients shape phytoplankton communities, particularly through phosphorus limitation. In this study, metatranscriptomic and metabarcoding approaches, complemented by light microscopy, were used to investigate the taxonomic composition and functional dynamics of the phytoplankton community in the northern Adriatic Sea, with a focus on toxic and potentially toxic genera. Monthly sampling, from April 2021 to January 2023, was conducted at two coastal stations. The three-method approach enabled differentiation between the two stations according to presence and metabolic contribution of toxic and potentially toxic genera. We demonstrate that molecular approaches (metatranscriptomics and metabarcoding) nearly doubled the detected species richness compared to traditional microscopy, highlighting a significant underestimation of cryptic, nanoplanktonic, and toxigenic species in current monitoring frameworks. Metatranscriptomic data reveal that many HAB taxa maintain active metabolic states throughout the year, even when their biomass is undetectable by light microscopy, suggesting the persistence of low-abundance active populations rather than exclusive reliance on quiescent resting stages.For the studied area, Pseudo-nitzschia species metabolically dominated the autumn diatom bloom. In spring 2021, a Noctiluca outbreak was detected, along with most other toxic and potentially toxic dinoflagellate genera recorded during the study period, notably Alexandrium, Amphidinium, Azadinium, Dinophysis, Gambierdiscus and Karenia. The results indicate that intense N. scintillans blooms markedly reshape phytoplankton metabolic activity, with implications for nutrient and carbon cycling.Based on patterns of metabolic pathway activity, including photosynthesis, carbon fixation, nitrogen metabolism, glycolysis, and oxidative phosphorylation, together with associated physiological responses, we identified contrasting life strategies and adaptive responses among phytoplankton taxa. This study provides critical new insights into the inventory of toxic species and their metabolic activities in the Northern Adriatic, including the detection of several toxigenic and potentially invasive species previously unrecorded or poorly resolved in the region, such as Azadinium poporum, Karlodinium veneficum, Gambierdiscus australes, and Prymnesium parvum. However, the results also underscore the need for further long term, multi-method research to fully understand the ongoing dramatic ecological changes in the northern Adriatic ecosystem in particular with respect to HAB species.

Mucilage aggregation is a striking phenomenon in the northern Adriatic Sea, reappearing massively in surface waters on the Istrian coast in 2024 after 20 years. Formed through polymerization of exuded sugars during microphytoplankton blooms, mucilage events are hard to capture with traditional monitoring. Here, we used real-time in situ sensors, satellite data and daily pulse-shape flow cytometry to analyze phytoplankton dynamics during this event. Mucilage formation was linked to rising temperatures and Po River-induced salinity drops. Microphytoplankton species like Cerataulina pelagica, Cylindrotheca closterium, Thalassionema spp., and Gonyaulax fragilis showed as important taxa in each different phase of the phenomenon. Aggregates consisted mainly of single cells. Mucilage periods featured low diversity and thicker, more complex cells, unlike autumn blooms which showed higher diversity, chain-forming colonies, and more pigments. Our findings highlight the key role of microphytoplankton and single cells in mucilage dynamics and the influence of environmental factors like temperature, wind and freshwater inputs on phytoplankton structure and biomass in coastal ecosystems.

We present Citizen Science-based Jellyfish Observation Initiatives (CS JOIs) across the Mediterranean Basin and propose a path toward standardization of the data they produce. We explored data collection and management through a shared database schema. Using an expert opinion questionnaire and adhering to standards that are recognized globally (e.g., by GBIF, OBIS, and EMODnet) such as Darwin Core and IOOS terminology, we propose a three-stage approach toward data management and standardization. JOIs vary in purpose, function, language, data collection, validation methodology, outreach, and levels of citizen engagement and training. This diversity presents unique opportunities and challenges for data collection and management. JOIs typically combine the dual role of providing real-time alert systems and enhancing our long-term knowledge of jellyfish distribution and, eventually, ecology. When global reporting systems are considered, local initiative identity, language, purpose, and community must be preserved to allow meaningful CS processes to evolve, while the integration of JOIs within them (and data collection and management in general) must be performed via standardized and shared methodologies. Finally, we discuss the contribution of novel technologies toward improving the activities and management of JOIs worldwide.

Four jellyfish species, ctenophoran Mnemiopsis leidyi and scyphozoan Cotylorhiza tuberculata, Chrysoara hysoscella and Rhizostoma pulmo were collected in summer of 2017 in the Gulf of Trieste (northern Adriatic Sea) and analysed for Hg and other metal(loid)s to assess their bioaccumulation and biomonitoring potential. No significant differences in Hg levels (0.06-0.22 µg/g dry mass) were observed between the studied species but all significantly concentrated Hg well above the dissolved Hg seawater levels (5 ng/L) of the gulf. The studied species have diverse diets consisting primarily of various plankton groups. C. hysoscella feeds mainly on mesozooplankton (>200 µm) R. pulmo and C. tuberculata mostly consume microzooplankton (50-200 µm) while M. leidyi preys on various organism (and particles) in the water column. In addition, C. tuberculata harbours autotrophic endosymbionts (microalgae). Considering their feeding behaviour, it appears that studied jellyfish species do not bioaccumulate Hg, nor other metal(loid)s, along the pelagic food web. Hence, the Hg levels in jellyfish are probably the consequence of the dissolved metal (passive and active) uptake. Moreover, the methodological approach analysing the jellyfish freeze-dried samples containing salt can distort the real picture and the Hg/Corg. ratio could better describe the metal level in the gelatinous organism. However, considering the high Hg bioconcentration factor (log BCF >5), jellyfish can be used aa a useful bioindicator for Hg, and other metal(loid)s, dissolved in seawater. Keywords: Jellyfish, coastal waters, mercury, bioconcentration, contamination, bioindicator

Jellyfish are considered important predators that play a key role in the organic matter cycling when they occur in blooms. Although their diet can vary spatially and temporally and be species-specific, mesozooplankton are generally recognised as important prey for various macrojellyfish. We present data from a long-term study (1974-2019) comparing the mesozooplankton biomass and blooms of four regularly occurring Scyphozoa species (Aurelia solida, Cotylorhiza tuberculata, Pelagia noctiluca, Rhizostoma pulmo) in the northern Adriatic, and since 2016, also of the invasive Ctenophora Mnemiopsis leidyi. The results showed large inter-annual variations in zooplankton biomass: annual dry mass geomean varied between 9.9 mg/m3 in 2016 and 49.9 mg/m3 in 1992, with 73% of the results below 20 mg/m3, while zooplankton carbon levels ranged between 0.2 and 22.7 mg/m3. In the period 1974-2019, there were years without massive jellyfish blooms and years in which several species occurred "en masse" in different seasons and/or together: A. solida in winter-spring, C. tuberculata in summer, R. pulmo in autumn-winter-spring and M. leidyi in summer-autumn. The Kruskal–Wallis test (p=0.0016) and Dunn's post-hoc multiple pairwise comparison test revealed significant differences in zooplankton biomass between years without blooms or single-species blooms of short duration and those with multi-species blooms with a cumulative duration of > 1 month.

The Northern Adriatic is a dynamic and the most productive part of the Adriatic Sea. The phytoplankton of the Northern Adriatic is, as many studies in this area showed, under heavy influence of freshwater inputs and anthropogenic pressures. Cluster analysis of a more than 20 year phytoplankton data set across steep spatio-temporal, ecological gradients on a longitudinal transect across the northern Adriatic, allowed us to identify significant and reoccurring phytoplankton species assemblages. Those phytoplankton clusters show stable seasonality and relation to environmental conditions and are presumed to be cornerstones of important ecosystem services provided by phytoplankton. Our results demonstrate that the stable seasonality of important phytoplankton clusters is disrupted, leading to a destabilisation of seasonal patterns in the biodiversity of primary producers. During the last 20 years, clusters characterised by dominating species were replaced by clusters characterised by the coexistence of several species. Overall the frequency of dense blooms of single species appears to decline. Multivariate analysis showed that possible reasons might lie in oligotrophication and increased salinity dynamics. Our results suggest the importance and applicability of cluster analysis in taxon based biodiversity long term data sets to elucidate functional biodiversity changes.

Plankton studies serve as a basis for marine ecosystem research, but knowledge of marine plankton is still incomplete due to its extreme taxonomic and functional complexity. The application of metabarcoding is very valuable for the characterisation of the plankton community. The plankton community of the Southern Adriatic is subject to strong environmental fluctuations and changes, which underlines the need for frequent, reliable and comprehensive characterisation of the plankton. The aim of this study was to determine the taxonomic composition and seasonal distribution of eukaryotic plankton in the Southern Adriatic. Plankton samples were collected monthly for one year at the coastal station of the Southern Adriatic and metabarcoding was used for taxonomic identification. The results showed a high taxonomic diversity and dynamic seasonal distribution patterns for both the protist and metazoan plankton communities. Metabarcoding revealed both the core, year-round plankton community and previously unrecorded plankton organisms in the Southern Adriatic. The results provide for the first time a comprehensive overview of the plankton community in this area by metabarcoding. The identified seasonal patterns of plankton genera and species in the Southern Adriatic will contribute to the understanding of plankton interactions and future changes in community diversity characterisation.

Marine microbial communities form the basis for the functioning of marine ecosystems and the conservation of biodiversity. With the application of metagenomics and metatranscriptomics in marine environmental studies, significant progress has been made in analysing the functioning of microbial communities as a whole. These molecular techniques are highly dependent on reliable, well-characterised, comprehensive and taxonomically diverse sequenced reference transcriptomes of microbial organisms. Here we present a set of 12 individual transcriptome assemblies derived from 6 representative diatom species from the northern Adriatic Sea grown under 2 environmentally relevant growth conditions (phosphate replete vs. phosphate deprived). After filtering the reads and assembly, an average number of 64,932 transcripts per assembly was obtained, of which an average of 8856 were assigned to functionally known proteins. Of all assigned transcripts, an average of 6483 proteins were taxonomically assigned to diatoms (Bacillariophyta). On average, a higher number of assigned proteins was detected in the transcriptome assemblies of diatoms grown under replete media condition. On average, 50% of the mapped proteins were shared between the two growth conditions. All recorded proteins in the dataset were classified into 24 COG categories, with approximately 25% belonging to the unknown function and the remaining 75% belonging to all other categories. The resulting diatom reference database for the northern Adriatic, focussing on the response to nutrient limitation as characteristic for the region and predicted for the future world oceans, provides a valuable resource for analysing environmental metatranscriptome and metagenome data. Each northern Adriatic transcriptome can also be used by itself as a reference database for the (meta)transcriptomes and gene expression studies of the associated species that will be generated in the future.

The northern Adriatic is characterised as the coldest and most productive marine area of the Mediterranean, which is due to high nutrient levels introduced by river discharges, the largest of which is the Italian Po River (at the same time also the largest freshwater input into the Mediterranean). The northern Adriatic is a very shallow marine ecosystem with ocean current patterns that result in long retention times of plankton in the area. The northern Adriatic phytoplankton biodiversity and abundance are well-studied, through many scientific and long-term monitoring reports. These datasets were based on phytoplankton morphological traits traditionally obtained with light microscopy. The most recent comprehensive eastern Adriatic phytoplankton checklist was published more than 20 years ago and is still valuable today. Since phytoplankton taxonomy and systematics are constantly being reviewed (partly also due to new molecular methods of species identification that complement classical methodologies), checklists need to be updated and complemented. Today, metabarcoding of molecular markers gains more and more importance in biodiversity research and monitoring. Here, we report the use of high throughput sequencing methods to re-examine taxonomic richness and provide updated knowledge of phytoplankton diversity in the eastern northern Adriatic to complement the standardised light microscopy method.This study aimed to report an up-to-date list of the phytoplankton taxonomic richness and phylogenetic relationships in the eastern northern Adriatic, based on sequence variability of barcoding genes resolved with advanced molecular tools, namely metabarcoding. Here, metabarcoding is used to complement standardised light microscopy to advance conventional monitoring and research of phytoplankton communities for the purpose of assessing biodiversity and the status of the marine environments. Monthly two-year net sampling targeted six phytoplankton groups including Bacillariophyceae (diatoms) and Chrysophyceae (golden algae) belonging to Ochrophyta, Dinophyceae (dinoflagellates), Cryptophyceae (cryptophytes), Haptophyta (mostly coccolithophorids) and Chlorophyta with Prasinophyceae (prasinophytes) and Chlorophyceae (protist green algae). Generated sequence data were taxonomically assigned and redistributed in two kingdoms, five classes, 32 orders, 49 families and 67 genera. The most diverse group were dinoflagellates, comprising of 34 found genera (48.3%), following by diatoms with 23 (35.4%) and coccolithophorids with three genera (4.0%). In terms of genetic diversity, results were a bit different: a great majority of sequences with one nucleotide tolerance (ASVs, Amplicon sequence variants) assigned to species or genus level were dinoflagellates (83.8%), 13.7% diatoms and 1.6% Chlorophyta, respectively. Although many taxa have not been detected that have been considered as common in this area, metabarcoding revealed five diatoms and 20 dinoflagellate genera that were not reported in previous checklists, along with a few species from other targeted groups that have been reported previously. We here describe the first comprehensive 18S metabarcode inventory for the northern Adriatic Sea.

Heterotrophic flagellates (HF) represent an important protist group in marine ecosystem functioning. Characterised by high taxonomic diversity, identification and classification of HF is often difficult using classical methods of light microscopy (LM). Complementing LM with molecular methods, such as barcoding, enables reliable taxonomic identification of even small size nanoflagellates that share similar or unnoticeable morphological features. The order Bicosoecida is a group of heterotrophic nanoflagellates that are important part of protist plankton and benthic communities of the world oceans. Recently, on the basis of high-resolution light microscopy and barcoding, a new bicosoecid genus, Bilabrum, was described with B. latius sp. as a type species. Our study reports on identification of B. latius from co-culture with the diatom species Chaetoceros affinis isolated from fresh plankton samples collected in the southern Adriatic. This detection of the Adriatic B.latius represents first record of this species outside itś up to now known and described habitat (deep-sea sediment of the South - East Atlantic Ocean) and in diatom co-culture.

This manuscript presents four new observations of the jellyfish Mawia benovici in the Adriatic Sea. This new species was recently identified as Pelagia benovici by Piraino et al. (2014) and then placed in the new genus Mawia by Avian et al. 2016. This species is rare and is almost exclusively observed in the Adriatic Sea. Interestingly, the majority of observations refer to males only. Few studies have addressed the issue of sex determination in Syphozoa in particular, as sex identity can only be determined at the medusa stage. Unfortunately, the rarity of M. benovici and the lack of female specimens have so far prevented indispensable laboratory studies to clarify its life cycle. Still, we tried to propose an explanation for our field observations.

Mesozooplankton and gelatinous zooplankton communities in Chesapeake Bay (CB) and the northern Adriatic Sea (NAS) have been subject to similar stressors over recent decades, including warming waters, overfishing, urbanization, and eutrophication. Direct comparisons between the systems are clouded by the lack of standardized and sustained long-term monitoring programs in both, which have covered different temporal and spatial scales, and employed different methodologies. Data that are available show that the systems differ in community composition, with CB having fewer species compared with the more diverse NAS. Both systems have seen an altered gelatinous zooplankton community over recent decades. In the NAS, these changes in part have been due to the recent introduction of nonindigenous species, a phenomenon not yet documented in CB. Chesapeake Bay has seen a long-term decline in the abundance of the dominant copepod taxa, attributed to increases in ctenophore abundance and/or increased seasonal hypoxia. Given the importance of mesozooplankton and gelatinous organisms in marine food webs, it is imperative that future ecosystem-based management efforts for marine resources include coordinated, consistent, and standardized monitoring of mesozooplankton and gelatinous zooplankton. Such data would allow for the development of robust indices to help achieve management goals for water quality, ecosystem health, and marine resources.

One of the obstacles to detecting regional trends in jellyfish populations is the lack of a defined baseline. In the Adriatic Sea, the jellyfish fauna (Scyphozoa and Ctenophora) is poorly studied compared to other taxa. Therefore, our goal was to collect and systematize all available data and provide a baseline for future studies. Here we present phenological data and relative abundances of jellyfish based on 2010–2019 scientific surveys and a “citizen science” sighting program along the eastern Adriatic. Inter-annual variability, seasonality and spatial distribution patterns of Scyphomedusae and Ctenophore species were described and compared with existing historical literature. Mass occurrences with a clear seasonal pattern and related to the geographical location were observed for meroplanktonic Scyphomedusae Aurelia solida, Rhizostoma pulmo, and to a lesser extent Chrysaora hysoscella, Cotylorhiza tuberculata and Discomedusa lobata. Holoplanktonic Pelagia noctiluca also formed large aggregations, which were seasonally less predictable and restricted to the central and southern Adriatic. Four species of Ctenophora produced blooms limited to a few areas: Bolinopsis vitrea, Leucothea multicornis, Cestum veneris and the non-native Mnemiopsis leidyi. However, differences between Adriatic subregions have become less pronounced since 2014. Our results suggest that gelatinous organisms are assuming an increasingly important role in the Adriatic ecosystem, which may alter the balance of the food web and lead to harmful and undesirable effects.

A semi- quantitative time series (2013-2017) was used to present the recent events of scyphomedusae appearance and abundance in the Boka Kotorska Bay, Montenegro, Southeast Adriatic. Six meroplanktonic species were recorded: Aurelia spp, Chrysaora hysoscella, Cotylorhiza tuberculata ̧ Discomedusa lobata, Drymonema dalmatinum and Rhizostoma pulmo. Among them, C. hysoscella and D. lobata dominated in the water column during winter and spring, forming dense aggregations in March and May, and February to May, respectively. Our description of the D. lobata blooms are actually the first known records of blooms for this species. C. tuberculata was observed in the Bay principally in August and September. The bloom was occurred only in 2017, being the first information of C. tuberculata mass appearance in this area. We hypothesized that global warming phenomena could trigger the observed changes, and in this respect, long-term trends of sea surface temperature (SST) fluctuations were analysed. The scyphomedusae blooms coincided with high positive SST anomalies, noted in the last seven years for this area. To better understand the mechanisms underlying changes in their phenology and abundance, detailed studies on benthic stages in the Bay are essential.